7.3 Translation And Protein Structure

Question 1

what are ribosomes made of?+reasons (2)

Answer 1

proteins (for stability)
ribosomal RNA (for catalytic activity)

Question 2

what do ribosomes consist of? (2)

Answer 2

• small ribosomal subunit contains mRNA biding site
• large subunit contains tRNA binding site (A (aminoacyl) site, P (peptidyl) site, E (exit) site)

Question 3

where can ribosomes be found?

Answer 3

found freely flouting in cytosol
bound to rough ER

Question 4

what are the four key regions of tRNA (clover shape)? and what do they do?

Answer 4

• acceptor stem (carries an amino acid)
• anticodon (associates with the mRNA codon (via complementary base pairings))
• t arm associates with ribosome (via, E, P and A binding sites)
• d arm associates w/ tRNA activating enzyme (responsible for adding amino acid to acceptor stem)

Question 5

what does each tRNA bind to?

Answer 5

a specific amino acid in the cytoplasm in a reaction catalysed by tRNA activating enzyme
- each amino acid is recognised by a specific enzyme

Question 6

what is the two step process of the binding of the amino acid to the tRNA acceptor stem? (2)

Answer 6

• the enzyme binds ATP to the tRNA acceptor to form an amino acid AMP complex linked by high energy bond (PP released)
• amino acid is coupled to tRNA and AMP is released and tRNA is now ready for use

Question 7

what is the purpose enzyme binding ATP (phosphorylation) in this process? (2)

Answer 7

• create a high energy bond that is transferred to tRNA molecule
• the store energy will provide majority of energy required for peptide bond formation during translation

Question 8

what is the process of translation? (12)

Answer 8

INITIATION
1. Small ribosomal subunit binds to the 5’ end of mRNA and moves it along until it reaches a start codon (AUG)
2. the appropriate tRNA molecule binds to the codon via its anticodon (according to complementary base pairings)
3. large ribosomal subunit align itself to the tRNA molecule at the P site and forms a complex w/ small subunit
ELONGATION
1. second tRNA molecule pairs with the next codon in the ribosomal A site
2. the amino acid in the P site is covalently attached via peptide bond (condensation reaction) to the amino acid in the A site
3. the tRNA in the P site is deacylated (no amino acid) while tRNA in the A site carries the peptide chain
TRANSLOCATION
1. the ribosome moves along the mRNA strand by one codon positions (5’->3’)
2. deacylated tRNA moves into E site and released, while tRNA carrying the peptide chain moves to the P site
3. another tRNA molecule attaches to the next codon in the now unoccupied A site and process is repeated
TERMINATION
1. elongation and translocation continue in repeated cycle until ribosome reaches stop codon
2. the codons don’t recruit a tRNA molecule , but recruit a release factor that signals for translation to stop
3. The polypeptide is released and the ribosome disassembles back into 2 independent subunits

Question 9

in eukaryotes what separates genetic material from the ribosome?

Answer 9

nucleus

Question 10

how is mRNA transported to the nucleus? (2)

Answer 10

• after transcription, the mRNA molecule is transported from the nucleus (via nuclear pores) prior to translation
• the transport requires modification of RNA construct (eg, 5’- methyl capping and 3’-polyadenylation)

Question 11

why does transcription and translation not have not have to separated in prokaryotes?

Answer 11

they lack comparmentalised structures

Question 12

how does transcription and translation occur in prokaryotes? (2)

Answer 12

• ribosome begins translating mRNA while it is still being transcribed from the DNA template
• this is possible because both transcription and translation occur in 5’-> 3’ direction

Question 13

what is a polysome?

Answer 13

a group of 2 or more ribosome translating an mRNA sequence simultaneously

Question 14

how may polysomes form in prokaryotes?

Answer 14

form whilst mRNA is still being transcribed from the DNA template

Question 15

what will ribosomes on the 3’-end of the polysome cluster look like compared to the 5’-end?

Answer 15

3’-end will have longer polypeptide chains than those on the 5’-end

Question 16

where are all proteins produced by eukaryotic cells initially synthesised?

Answer 16

in the cytosol

Question 17

where does the protein go if it is targeted for intracellular use within in the cytosol?

Answer 17

• the ribosome remains free and unattached

Question 18

where does the protein go if it is targeted for secretion, membrane fixation or use in lysosomes?

Answer 18

ribosome becomes bound to ER

Question 19

how is protein destination determined?

Answer 19

by presence / absence of initial signal sequence on nascent polypeptide chain

Question 20

what does the presence of signal result in? (5)

Answer 20

• results in the recruitment of a signal recognition particle (SRP), halts translation
• the SRP-ribosome complex then docks at a receptor located on the ER membrane, (forming rough ER)
  translation is re-initiated and the polypeptide chain continues to grow via a transport channel into the lumen of the ER
  -> the synthesised protein will be transported via a vesicle to Golgi complex for secretion or lysosome
  -> proteins targeted for membrane fixation (eg integral proteins) get embedded in ER membrane
• the signal sequence is cleaved and the SRP recylces once the polypeptide is completely synthesised within the ER

Question 21

what is the primary structure of proteins? (2)

Answer 21

• first level of structural organisation in a protein is the sequence of amino acids which comprise the polypeptide chain
• formed by covalent polypeptide bonds between the amine and carboxyl groups of adjacent amino acids

Question 22

why does the primary structure control the subsequent levels of protein organisation?

Answer 22

it determines the nature of the interactions between R groups of different amino acids

Question 23

what is the secondary structure? (3)

Answer 23

• the way a poylpeptide chain folds in a repeated arrangement to form a-helices and b-pleated sheets
• a result of the h-bonds between amine and carboxyl groups of non-adjacent amino acids
  (sequences that don’t form a-helices or b-pleated sheets exist as random coil)
• secondary structure provides polypeptide chain with level of mechanical stability

Question 24

what is the tertiary structure? (3)

Answer 24

• the way polypeptide chain coils and turns to form complex molecular shape (eg. 3D)
• caused by interactions between R groups (including H-bonds, disulphide bridges, ionic bonds and hydrophobic interactions)
• relative amino acid positions are important (eg. non-polar amino acids usually avoid exposure to aqueous solutions)
  (tertiary structure may be important for function of protein)

Question 25

what is the quaternary structure?

Answer 25

• multiple polypeptide or prosthetic groups may interact to form a single, larger, biologically active protein
• prosthetic group = an inorganic compound involved in protein structure of function
• protein containing a prosthetic is called conjugated protein
• quaternary structure is held together by variety of bond (like tertiary)